v3.2.0

What's Changed

• Remove code related to nf-core Validation and update to nf-core Schema completed by @slsevilla in #83
• Expose nf-plugins; set version and plugin ID by @slsevilla with 6e58b0c
• update config to handle RHEL8 environment
• Convert from check_max to resourceLimits by @SuchiC23 and @slsevilla with 6d09ae3

Full Changelog: v3.1.0...v3.2.0

v3.1.0

What's Changed

• updated the usage documents @SuchiC23 #75
• Added iontorrent sample sheet information @SuchiC23 #74
• Updated the Multiqc to version 1.25.1 @SuchiC23 #72
• fix typo in samplesheet @slsevilla in #78
• add iontorrent test to CI/CD @slsevilla in #78
• reformat, add platform names to docs @slsevilla in #78

New Contributors

• @SuchiC23 made their first contribution in #74

Full Changelog: v3.0.0...v3.1.0

v3.0.0

What's Changed

• Feature docs by @arunbodd in #56
• NF-core template update, added three new entry points by @slsevilla in #60
• Added CI workflow to test the pipeline by @antongray1 in #62
• Updated readme to trigger mkdocs workflow by @antongray1 in #65
• Removed redundant code by @slsevilla in f879ac3
• Updated FREYJA version by @slsevilla in 7d615c8 (fixes #58)
• Removed IVAR Variant calling in c016987 (fixes #61 )
• Removed Samtools FAIDX by @slsevilla in c8163ad (fixes #71 )
• Update schema requirements by @slsevilla in f98393a
• Fix samplesheet col name inconsistency by @slsevilla in 2a511d6 (issue #66 )
• Fixes docker issue by adding quay.io by @slsevilla in e0066f1 (issue #68)

New Contributors

• @antongray1 made their first contribution in #62

Full Changelog: v2.3.1...v3.0.0

v2.3.1

What's Changed

• added awk to assign gff_feature to freyja - variant calls by @arunbodd in #53

Full Changelog: v2.3.0...v2.3.1

v2.3.0

What's Changed

• chore: remove conflicting code by @arunbodd in #51
• Add test profile for ONT data, add test data, update configs, cleanup gitignore files by @slsevilla in #49
• Rebase dev from testprofiles, add new config by @arunbodd in #50
• Rebasing dev to main after issues with previous merge by @slsevilla in #52

Full Changelog: v2.2.1...v2.3.0

v2.2.0

What's Changed

• Re: Reheader Bam issue addressed by @arunbodd in #40
• Merge pull request #40 from CDCgov/dev by @arunbodd in #47
• Update images, samplesheet updates, rehead BAM by @slsevilla in #45

Full Changelog: v2.1.0...v2.2.0

v2.1.0

What's Changed

• Updated README and user-docs by @slsevilla @arunbodd in #29, #30, #33
• Feature Add: Amino Acid calling, threshold features added #27 by @arunbodd @schavan023 in #31

Full Changelog: v2.0.0...v2.1.0

v2.0.0

What's Changed

• Update README.md by @SMorrison42 in #12
• Hseabolt patch 1 by @slsevilla in #25
• Docs Overhaul, CI addition, IVAR feat add by @slsevilla in #21
• feat: Added processing of Ion-torrent Bams and ONT long reads
• feat: Added Nanoplot as Quality metrics tool for ONT long reads
• feat: Samtools ampliconclip is used as primary trimming tool for ONT-long reads.
• fix: removed ivar trim which was erroring for ONT-long reads
• refactor: specify primer bed file as 7th column in samplesheet - refer to ReadME file
• refactor: Qualimap Bamqc and Ivar variant calling now use "gff" file as one of the parameters, instead of bed or gff3 file formats.
• fix: Removed parameter --fai (fasta index), it now builds using samtools faidx
• feat: MultiQC report shows Freyja Demix results.
• feat: fasta and gff are now defaulted to assets folder. User input required to change these references (We strongly suggest users * * not to use a different reference, as it may lead to accession ID conflicts downstream)
• docs: updated README
• docs: update CHANGELOG format
• docs: created a VERSION log
• ci: added github actions for deployment

New Contributors

• @SMorrison42 made their first contribution in #12
• @slsevilla made their first contribution in #25

Full Changelog: 1.0.0...v2.0.0

1.0.0

Initial release of Aquascope 1.0.0